Use augur merge #75
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Use augur merge #75
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Narrows the scope of the append_usvi rule to just merging data files.
Use our own tooling designed for this type of operation. There is a slight change in behavior: augur merge adds quotes around values with spaces whereas csvtk doesn't, but I think that's ok.
This better reflects the duplicate handling used by augur merge. In case of duplicates, augur merge will keep the last one from the input list. seqkit rmdup keeps the first one from the input list so the order is reversed. There are some behavior changes, none of which should have any impact on downstream usage: 1. The order of sequences in the file is reversed on a file level. 2. seqkit's default behavior wraps lines at 60 characters.
genehack
approved these changes
Dec 9, 2024
j23414
approved these changes
Dec 9, 2024
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Agree with your changes and ran a quick test:
Findings: USVI records were merged in as expected, node callout links work as expected, the difference in quoting does not seem to affect the auspice view. Good, thank you!
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Description of proposed changes
Use our own tooling designed for this type of operation. Details in commits.
Related issue(s)
augur mergeto spike in USVI records #73Checklist